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NM_003718.5(CDK13):c.2563G>A (p.Asp855Asn) AND Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Germline classification:
Likely pathogenic (1 submission)
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001823487.3

Allele description [Variation Report for NM_003718.5(CDK13):c.2563G>A (p.Asp855Asn)]

NM_003718.5(CDK13):c.2563G>A (p.Asp855Asn)

Gene:
CDK13:cyclin dependent kinase 13 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p14.1
Genomic location:
Preferred name:
NM_003718.5(CDK13):c.2563G>A (p.Asp855Asn)
HGVS:
  • NC_000007.14:g.40047840G>A
  • NG_052965.1:g.102481G>A
  • NM_003718.5:c.2563G>AMANE SELECT
  • NM_031267.3:c.2563G>A
  • NP_003709.3:p.Asp855Asn
  • NP_112557.2:p.Asp855Asn
  • NC_000007.13:g.40087439G>A
  • NM_003718.4:c.[2563G>A]
Protein change:
D855N
Links:
dbSNP: rs2150517037
NCBI 1000 Genomes Browser:
rs2150517037
Molecular consequence:
  • NM_003718.5:c.2563G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_031267.3:c.2563G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD)
Identifiers:
MONDO: MONDO:0044302; MedGen: C4479246; OMIM: 617360

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002072956Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002072956.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant p.D855N in CDK13 (NM_003718.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant is present in the protein kinase domain wherein previously disease causing missense mutations have been reported (Hamilton MJ et al). The p.D855N variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.D855N missense variant is predicted to be damaging by both SIFT and PolyPhen2. The aspartic acid residue at codon 855 of CDK13 is conserved in all mammalian species. The nucleotide c.2563 in CDK13 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 6, 2024